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TopHat-Recondition: a post-processor for TopHat unmapped reads
Christian Brueffer1, Lao H Saal2
1Division of Oncology and Pathology, Department of Clinical Sciences, Lund University Cancer Center, Lund University, Medicon Village Building 404-B2, Lund, 223 81, Sweden.
BMC Bioinformatics
|May 5, 2016
Summary
TopHat-Recondition is a new tool that fixes unmapped reads from the TopHat software, ensuring compatibility with other bioinformatics tools. This improves RNA sequencing data analysis by allowing seamless processing of BAM files.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- TopHat is a widely used tool for mapping RNA sequencing data, generating output in the Binary Alignment/Map (BAM) format.
- The BAM format is crucial for the exchange and analysis of aligned sequencing reads, making format compliance essential for interoperability.
- A known issue is that TopHat's handling of unmapped reads creates files incompatible with other SAM/BAM format-compliant software.
Purpose of the Study:
- To address the incompatibility issue with TopHat's unmapped reads.
- To develop a solution that enables downstream analysis of all reads processed by TopHat.
Main Methods:
- Development of TopHat-Recondition, a post-processing tool.
- Implementation of format correction for TopHat's unmapped reads.
Main Results:
- TopHat-Recondition successfully repairs TopHat's unmapped read files.
- The repaired files are compatible with standard SAM/BAM format-compliant software.
Conclusions:
- TopHat-Recondition resolves the unmapped read compatibility problem for TopHat.
- The software is freely available on GitHub under a 2-clause BSD license, promoting wider adoption and analysis of RNA sequencing data.
